Home >
Community >
Regarding MD simulation? what apo proteins are meaning and ligand...
Upvote
25
Downvote
+ Molecular dynamics simulation
+ Ligand
+ Microsoft office excel
Posted by
Mark Lambert
Regarding MD simulation? what apo proteins are meaning and ligand...
Sutanu Mukhopadhyay Thank you Viya, I got it, I will generate RMSD, RMSF, RG, SASA for all the ligand-protein complex. Then again will repeat only for the holo protein. Then finally incorporate everything in a single graph (module wise, like one for RMSD, One for RMSF) to compare, to state the initial and final flexibility, stability at different time frames.
Sutanu Mukhopadhyay Thank you Viya, I got it, I will generate RMSD, RMSF, RG, SASA for all the ligand-protein complex. Then again will repeat only for the holo protein. Then finally incorporate everything in a single graph (module wise, like one for RMSD, One for RMSF) to compare, to state the initial and final flexibility, stability at different time frames.
"Apo" simply means the protein structure without any ligand and "Holo" stands for the protein-ligand complex. People generally compare the parameters (such as RMSD/ RMSF/ RoG/ SASA etc.) with respect to the apo structure, i.e., what changes occur before and after ligand binding and how it effects the protein dynamics. It's advisable to plot the apo protein and all the protein-ligand complexes in a single plot to compare them, you may also make histograms. Grace/ XmGrace is a suitable software.
"Apo" simply means the protein structure without any ligand and "Holo" stands for the protein-ligand complex. People generally compare the parameters (such as RMSD/ RMSF/ RoG/ SASA etc.) with respect to the apo structure, i.e., what changes occur before and after ligand binding and how it effects the protein dynamics. It's advisable to plot the apo protein and all the protein-ligand complexes in a single plot to compare them, you may also make histograms. Grace/ XmGrace is a suitable software.
Sutanu Mukhopadhyay Thank you Viya, I got it, I will generate RMSD, RMSF, RG, SASA for all the ligand-protein complex. Then again will repeat only for the holo protein. Then finally incorporate everything in a single graph (module wise, like one for RMSD, One for RMSF) to compare, to state the initial and final flexibility, stability at different time frames.
Sutanu Mukhopadhyay Thank you Viya, I got it, I will generate RMSD, RMSF, RG, SASA for all the ligand-protein complex. Then again will repeat only for the holo protein. Then finally incorporate everything in a single graph (module wise, like one for RMSD, One for RMSF) to compare, to state the initial and final flexibility, stability at different time frames.
More
VOTE
"Apo" simply means the protein structure without any ligand and "Holo" stands for the protein-ligand complex. People generally compare the parameters (such as RMSD/ RMSF/ RoG/ SASA etc.) with respect to the apo structure, i.e., what changes occur before and after ligand binding and how it effects the protein dynamics. It's advisable to plot the apo protein and all the protein-ligand complexes in a single plot to compare them, you may also make histograms. Grace/ XmGrace is a suitable software.
"Apo" simply means the protein structure without any ligand and "Holo" stands for the protein-ligand complex. People generally compare the parameters (such as RMSD/ RMSF/ RoG/ SASA etc.) with respect to the apo structure, i.e., what changes occur before and after ligand binding and how it effects the protein dynamics. It's advisable to plot the apo protein and all the protein-ligand complexes in a single plot to compare them, you may also make histograms. Grace/ XmGrace is a suitable software.
More
VOTE